paired-end_read_rna_quantification_salmon_mapping

paired-end_read_rna_quantification_salmon_mapping.nf

Quantify RNA abundance in paired-end RNA reads using Salmon (mapping mode).

Inputs / Outputs

I/O	Description
Input	R1 and R2 fastq.gz files for each sample.
Output	Salmon output files including quant.sf and quant.genes.sf files for each sample.

Dependencies

• Salmon

Example

nexus run --nf-workflow paired-end_read_rna_quantification_salmon_mapping.nf \
    -c NEXTFLOW_CONFIG_FILE \
    -w WORK_DIR \
    --samples_tsv_file SAMPLES_TSV_FILE \
    --output_dir OUTPUT_DIR \
    --reference_transcripts_fasta_file REFERENCE_TRANSCRIPTS_FASTA_FILE \
    --params_salmon_index '"--gencode"' \
    --params_salmon_quant '"--libType IU --seqBias --gcBias --posBias"'

Usage

workflow:
    1. Quantify RNA in paired-end FASTQ files using Salmon.

usage: nexus run --nf-workflow paired-end_read_rna_quantification_salmon_mapping.nf [required] [optional] [--help]

required arguments:
    -c                                      :   Nextflow .config file.
    -w                                      :   Nextflow work directory path.
    --samples_tsv_file                      :   TSV file with the following columns:
                                                'sample_id', 'fastq_file_1', 'fastq_file_2'.
    --output_dir                            :   Directory to which output files will be copied.

optional arguments:
    --reference_transcripts_fasta_file      :   Reference transcripts FASTA file (default: /datastore/lbcfs/collaborations/pirl/seqdata/references/gencode.v41.transcripts.fa).
    --params_salmon_index                   :   Salmon index parameters (default: '"--gencode"').
                                                Note that the parameters need to be wrapped in quotes.
    --params_salmon_quant                   :   Salmon parameters (default: '"--libType IU --seqBias --gcBias --posBias"').
                                                Note that the parameters need to be wrapped in quotes.
    --delete_work_dir                       :   Delete work directory (default: false).

Parameters

-c

• Nextflow config file can be downloaded here

--samples_tsv_file

• A TSV (tab-separated values) file with the following headers:

Header	Description
sample_id	Sample ID.
fastq_file_1	Full path to R1 fastq.gz file
fastq_file_2	Full path to R2 fastq.gz file

--reference_transcripts_fasta_file

• Reference transcripts FASTA files can be found in /datastore/lbcfs/collaborations/pirl/seqdata/references/ on LBG.

--params_salmon_index

• Refer to the Salmon documentation.
• The following parameters for Salmon are already included in nexus module for salmon index and should not be specified:
  • --transcripts
  • --index
  • --threads

--params_salmon_quant

• Refer to the Salmon documentation.
• The following parameters for Salmon are already included in nexus module for salmon quant and should not be specified:
  • --index
  • --mates1
  • --mates2
  • --geneMap
  • --output
  • --threads